Contacts of the helix formed by residues 1030 - 1041 (chain C) in PDB entry 1AWV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO1030 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1026C ALA* 3.2 19.9 - - + +
1027C ASP 4.0 7.2 - - - +
1028C LYS 3.3 6.1 - - - +
1029C VAL* 1.3 86.7 - - - +
1031C LYS* 1.3 58.3 + - + +
1033C ALA* 3.8 0.9 - - + +
1034C GLU* 2.8 38.0 + - + +
1086C GLU* 3.1 17.7 - - - +
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Residues in contact with LYS1031 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029C VAL 3.4 1.0 - - - -
1030C PRO* 1.3 76.9 - - + +
1032C THR* 1.3 59.9 + - - +
1034C GLU* 4.9 0.9 - - - -
1035C ASN* 3.1 20.1 + - - +
1079C TYR* 2.9 59.6 + - + +
1083C PHE* 3.4 34.0 - - + +
1084C GLU* 3.1 30.1 + - - +
1086C GLU* 3.5 16.2 + - + +
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Residues in contact with THR1032 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029C VAL* 3.1 27.4 + - - +
1031C LYS* 1.3 76.9 - - - +
1033C ALA* 1.3 60.8 + - - +
1035C ASN* 3.8 2.4 + - - +
1036C PHE* 3.3 23.6 + - - +
1083C PHE* 4.3 16.9 - - + -
1086C GLU* 3.5 11.5 + - - +
1100C MET* 3.5 37.0 - - + +
1108C ASN* 6.1 0.7 - - - -
1127C VAL* 3.9 12.7 - - + +
1129C PHE* 3.5 21.0 - - + -
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Residues in contact with ALA1033 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004C PRO* 5.8 0.4 - - + -
1024C LEU* 3.8 14.5 - - + +
1025C PHE 3.9 5.2 - - - +
1026C ALA* 3.2 39.0 - - + +
1029C VAL* 2.8 17.8 + - + +
1030C PRO 3.8 0.9 - - - +
1032C THR* 1.3 76.2 - - - +
1034C GLU* 1.3 60.8 + - - +
1036C PHE 3.4 1.2 + - - -
1037C ARG* 2.9 30.7 + - - +
1129C PHE* 4.8 8.5 - - - +
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Residues in contact with GLU1034 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004C PRO* 5.2 1.4 - - - +
1026C ALA* 5.2 10.3 - - + +
1030C PRO* 2.8 23.0 + - + +
1031C LYS* 4.2 2.9 - - - +
1033C ALA* 1.3 73.5 - - - +
1035C ASN* 1.3 56.0 + - - +
1037C ARG* 2.8 47.3 + - - +
1038C ALA* 2.7 39.7 + - - +
1044C LYS* 5.8 1.6 + - - -
1078C ILE* 4.8 5.6 - - + -
1079C TYR* 4.4 6.3 - - - +
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Residues in contact with ASN1035 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1031C LYS 3.1 20.4 + - - +
1032C THR 3.8 5.2 + - - +
1033C ALA 3.2 0.2 - - - -
1034C GLU* 1.3 77.3 - - - +
1036C PHE* 1.3 58.5 + - - +
1038C ALA* 3.9 1.2 - - - +
1039C LEU* 3.0 43.8 + - - +
1048C TYR* 5.0 1.2 + - - -
1077C SER* 3.5 10.7 - - - -
1078C ILE* 3.5 31.3 + - - +
1079C TYR* 3.6 13.8 + - + +
1083C PHE* 3.5 26.2 - - + -
1100C MET* 3.9 13.1 - - - +
1109C GLY 3.6 10.5 + - - -
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Residues in contact with PHE1036 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C VAL* 3.6 18.8 - - + -
1008C PHE* 3.5 26.5 - + - -
1022C PHE* 4.6 4.0 - + - -
1024C LEU* 3.7 17.9 - - + -
1032C THR 3.3 9.8 + - - +
1033C ALA 4.0 2.7 - - - +
1035C ASN* 1.3 78.2 - - - +
1037C ARG* 1.3 60.3 + - - +
1039C LEU* 3.7 5.8 - - - +
1040C SER* 2.9 45.6 + - - -
1048C TYR* 3.5 22.0 - + - -
1098C LEU* 3.9 20.6 - - + -
1100C MET* 5.5 2.5 - - - -
1112C PHE* 3.6 31.9 - + + -
1129C PHE* 3.3 33.2 - + + -
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Residues in contact with ARG1037 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1004C PRO* 4.0 12.8 - - + -
1006C VAL* 3.9 20.2 - - + -
1024C LEU* 3.8 13.2 - - + +
1033C ALA 2.9 19.3 + - - +
1034C GLU* 2.8 42.3 + - - +
1036C PHE* 1.3 76.9 - - - +
1038C ALA* 1.3 64.7 - - - +
1040C SER* 2.9 19.6 + - - -
1041C THR* 3.1 20.2 + - - +
1043C GLU* 2.7 45.2 + - - -
1044C LYS* 5.6 0.8 - - - +
1163C GLN* 3.2 38.9 + - + +
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Residues in contact with ALA1038 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1034C GLU* 2.7 23.0 + - - +
1035C ASN 4.1 2.0 - - - +
1037C ARG* 1.3 77.4 - - - +
1039C LEU* 1.3 56.9 + - - +
1041C THR* 3.6 8.1 + - - -
1042C GLY* 3.1 23.0 + - - -
1043C GLU* 3.7 27.7 + - + +
1044C LYS* 4.3 12.1 + - + +
1046C PHE 4.5 1.9 - - - +
1078C ILE* 4.1 24.9 - - + -
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Residues in contact with LEU1039 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1035C ASN* 3.0 43.6 + - - +
1036C PHE 3.7 0.2 - - - +
1038C ALA* 1.3 77.7 - - - +
1040C SER* 1.3 60.7 + - - +
1041C THR 3.6 0.2 + - - -
1042C GLY 3.9 3.1 + - - -
1046C PHE* 3.7 34.8 - - + +
1047C GLY* 3.3 11.9 - - - -
1048C TYR* 3.1 62.8 + - + +
1049C LYS 4.9 0.5 + - - -
1067C PHE* 3.7 20.0 - - + -
1076C LYS 4.0 3.4 - - - +
1078C ILE* 4.1 8.3 - - + -
1110C SER* 3.8 14.6 - - - -
1161C CYS* 4.9 0.3 - - - -
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Residues in contact with SER1040 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1006C VAL* 4.0 21.8 - - - +
1008C PHE* 3.7 10.8 - - - -
1036C PHE* 2.9 40.8 + - - -
1037C ARG 2.9 6.5 + - - -
1039C LEU* 1.3 78.9 - - - +
1041C THR* 1.3 57.8 + - - +
1048C TYR* 3.6 12.1 - - - -
1161C CYS* 3.1 38.6 - - - +
1162C GLY* 4.2 2.5 - - - -
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Residues in contact with THR1041 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037C ARG* 3.1 14.9 + - + +
1038C ALA 3.6 2.4 + - - -
1040C SER* 1.3 79.4 - - - +
1042C GLY* 1.3 61.2 + - - +
1043C GLU* 2.7 41.3 + - - +
1161C CYS 4.6 3.3 - - - +
1162C GLY* 4.1 4.9 - - - -
1163C GLN* 3.6 40.8 - - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il